Weekly upstream merge.

.gitignore

@@ -6,4 +6,5 @@
 .idea
 build
 xcuserdata
-*.xcuserdata
+*.xcuserdata
+TARGET_BUILD_DIRTARGET_BUILD_DIR

Mothur.xcodeproj/project.pbxproj

@@ -9,6 +9,8 @@
 /* Begin PBXBuildFile section */
 		219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */; };
 		219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */; };
+		7B21820017AD777B00286E6A /* classifysvmsharedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */; };
+		7B21820317AD77BD00286E6A /* svm.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7B21820117AD77BD00286E6A /* svm.cpp */; };
 		7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
 		834D9D581656D7C400E7FAB9 /* regularizedrandomforest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */; };
 		834D9D5C1656DEC800E7FAB9 /* regularizeddecisiontree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */; };
@@ -401,6 +403,10 @@
 		219C1DE11552C508004209F9 /* newcommandtemplate.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = newcommandtemplate.h; sourceTree = "<group>"; };
 		219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcoremicrobiomecommand.cpp; sourceTree = "<group>"; };
 		219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getcoremicrobiomecommand.h; sourceTree = "<group>"; };
+		7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifysvmsharedcommand.cpp; sourceTree = "<group>"; };
+		7B2181FF17AD777B00286E6A /* classifysvmsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifysvmsharedcommand.h; sourceTree = "<group>"; };
+		7B21820117AD77BD00286E6A /* svm.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = svm.cpp; sourceTree = "<group>"; };
+		7B21820217AD77BD00286E6A /* svm.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = svm.hpp; sourceTree = "<group>"; };
 		7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
 		7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
 		7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = "<group>"; };
@@ -1155,6 +1161,7 @@
 		08FB7795FE84155DC02AAC07 /* Source */ = {
 			isa = PBXGroup;
 			children = (
+				7B17437A17AF6F02004C161B /* svm */,
 				A7A61F1A130035C800E05B6B /* LICENSE */,
 				A70332B512D3A13400761E33 /* makefile */,
 				A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */,
@@ -1276,6 +1283,17 @@
 			name = Products;
 			sourceTree = "<group>";
 		};
+		7B17437A17AF6F02004C161B /* svm */ = {
+			isa = PBXGroup;
+			children = (
+				7B21820117AD77BD00286E6A /* svm.cpp */,
+				7B21820217AD77BD00286E6A /* svm.hpp */,
+				7B2181FE17AD777B00286E6A /* classifysvmsharedcommand.cpp */,
+				7B2181FF17AD777B00286E6A /* classifysvmsharedcommand.h */,
+			);
+			name = svm;
+			sourceTree = "<group>";
+		};
 		A7386C191619C9FB00651424 /* randomforest */ = {
 			isa = PBXGroup;
 			children = (
@@ -2397,6 +2415,8 @@
 				A741744C175CD9B1007DF49B /* makelefsecommand.cpp in Sources */,
 				A7190B221768E0DF00A9AFA6 /* lefsecommand.cpp in Sources */,
 				A77916E8176F7F7600EEFE18 /* designmap.cpp in Sources */,
+				7B21820017AD777B00286E6A /* classifysvmsharedcommand.cpp in Sources */,
+				7B21820317AD77BD00286E6A /* svm.cpp in Sources */,
 				A7D9378A17B146B5001E90B0 /* wilcox.cpp in Sources */,
 				A7F24FC317EA36600021DC9A /* classifyrfsharedcommand.cpp in Sources */,
 				A747EC71181EA0F900345732 /* sracommand.cpp in Sources */,
@@ -2410,6 +2430,8 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				ALWAYS_SEARCH_USER_PATHS = NO;
+				CLANG_CXX_LANGUAGE_STANDARD = "gnu++0x";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				COPY_PHASE_STRIP = NO;
 				DEPLOYMENT_LOCATION = YES;
 				DSTROOT = TARGET_BUILD_DIR;
@@ -2428,6 +2450,8 @@
 			isa = XCBuildConfiguration;
 			buildSettings = {
 				ALWAYS_SEARCH_USER_PATHS = NO;
+				CLANG_CXX_LANGUAGE_STANDARD = "gnu++0x";
+				CLANG_CXX_LIBRARY = "compiler-default";
 				DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
 				DEPLOYMENT_LOCATION = YES;
 				DSTROOT = TARGET_BUILD_DIR;